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Journal of Clinical Microbiology, February 2003, p. 586-591, Vol. 41, No. 2
0095-1137/03/$08.00+0 DOI: 10.1128/JCM.41.2.586-591.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Staphylococci Unit,1 Collection of the Pasteur Institute, Institut Pasteur, 75724 Paris Cedex 15, France2
Received 29 August 2002/ Returned for modification 10 October 2002/ Accepted 1 November 2002
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Quinupristin-dalfopristin and the natural antibiotics produced by streptomycetes, such as streptogramin, pristinamycin, synergistin, mikamycin, and virginiamycin, are mixtures of two classes of compounds, A and B, with distinct primary structures (10, 14). The A compounds are polyunsaturated cyclic macrolactones, and the B compounds are cyclic hexadepsipeptides. Both types of compounds bind different targets in the peptidyltransferase domain of the 23S ribosomal subunit and inhibit protein elongation at different steps. Compounds A and B are bacteriostatic when used separately but act synergistically when combined, such that in some cases they are bactericidal, mainly against gram-positive bacteria.
In countries such as France, where natural mixtures (pristinamycin and synergistin) have been used orally and topically since 1960, the prevalence of clinical isolates of staphylococci resistant to mixtures of compounds A and B (pristinamycin MICs of >2 mg liter-1) varies from 0 to 44% in hospitals (22). Virginiamycin was long used in animal feed as a growth promoter in both Europe and the United States but was banned in Europe in 1999. The first staphylococcal clinical isolates resistant to the mixtures were reported in France in 1975 (14). Staphylococcal resistance to synergistic mixtures is always associated with resistance to A compounds (pristinamycin IIA MICs of
8 mg liter-1) but is not necessarily associated with resistance to B compounds (1).
In staphylococci, resistance to B compounds is mediated by (i) the methylation of 23S rRNA, which confers resistance to macrolide-lincosamide-streptogramin B (MLSB) when the erm genes are expressed constitutively (32); (ii) the hydrolysis of the drug by lyases (24) encoded by the vgbA (7) and vgbB (5) genes, which are always located on plasmids conferring resistance to A compounds; (iii) probable efflux ABC proteins encoded by the msr genes, which confers resistance to streptogramin B (SGB) and C14-C15 macrolides (26, 27); or (iv) a mutation in the L22 ribosomal protein of S. aureus, which is responsible for cross-resistance to SGB and erythromycin (23). Resistance to A compounds may be conferred by two categories of genes: (i) vatABCDE (4, 5, 8, 18, 25, 35), encoding related acetyltransferases that inactivate the drug and are found on staphylococcal and/or Enterococcus faecium plasmids, and (ii) vgaAB (2, 6) and lsa (28), encoding related ATP-binding proteins, the resistance mechanism of which has not been elucidated. vga-type genes are found in staphylococcal plasmids but not in E. faecium strains, whereas lsa conferring resistance to SGA and to clindamycin is present in the chromosome of all tested E. faecalis strains. A variant of vgaA (vgaAv) (19) carried by a transposon found in staphylococci, Tn5406 (20), which is located on plasmids and/or the chromosome, was recently characterized.
We have become aware of the vatA-vgbA combination (33; data not shown), which was not found in the 52 unrelated staphylococci tested previously (1). Indeed, vatA-vgbA was always associated with vgaA. Related plasmids (15 to 45 kb) carrying this combination have been detected in strains belonging to various staphylococcal species and isolated prior to 1997 (3).
The aim of the present study was to type and analyze the distribution of SGA resistance (SGAr) genes, because of their uncommon phenotype, in a collection of 62 SGAr clinical isolates of S. aureus sent to us from 1981 to 2001 by French hospital microbiologists.
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TABLE 1. Relevant characteristics of 62 S. aureus clinical isolates resistant to SGA
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Susceptibility to antimicrobial drugs. All clinical isolates were stored at -80°C and were isolated on Mueller-Hinton agar containing 10 µg of pristinamycin IIA ml-1. Susceptibility to antibiotics was determined by a disk diffusion assay with commercially available antibiotic disks (Bio-Rad), according to the recommendations of the French Society of Microbiology and with disks prepared in our laboratory as described previously (1). The MICs of vancomycin and teicoplanin were determined by the E-test according to the manufacturer's recommendations (AES, Combourg, France). A population analysis on brain heart infusion broth containing 4 mg of vancomycin liter-1 was carried out as previously described to screen for heterogeneous vancomycin intermediate S. aureus (hetero-VISA) strains (11).
DNA isolation and analysis. Total cellular DNA was isolated from staphylococcal strains and purified by using the QIAamps tissue kit from Qiagen (Hilden, Germany). S. aureus plasmid DNA was extracted and purified by using the QIAprep spin plasmid kit from Qiagen according to the manufacturer's instructions but with an additional step consisting of 1 h at 37°C in the presence of 10 µl of lysostaphin (1 mg ml-1). Restriction endonucleases were obtained from Amersham-Pharmacia Biotech, Inc. (Piscataway, N.J.) and used according to the manufacturer's instructions. Instagene matrix DNA preparations were used for PCR experiments according to the manufacturer's instructions (Bio-Rad). The DNA was digested with SmaI and subjected to pulsed-field gel electrophoresis as described previously (Fig. 1) (13). Concatameric bacteriophage lambda DNA molecules (48.5 kb; Bio-Rad) and the SmaI fragments of the cellular DNA from S. aureus NCTC 8325 were used as size standards. Macrorestriction fingerprints were compared visually and were scanned by using GelCompar II software (Applied Maths, Sint-Martens-Latem, Belgium). A similarity matrix was created by use of the band-based Dice similarity coefficient (tolerance of 1% and optimization of 2%). The unweighted pair-group method with average linkages was used to cluster the strains on the basis of the SmaI patterns. If the dendrograms revealed clusters that included strains with similarity of at least 80%, the patterns of the strains in the same cluster were compared visually on the same gel. The strains were clustered according to the following criteria proposed by Tenover et al. (31): (i) strains were grouped in the same major genotype if their patterns differed by no more than three bands (these strains were considered to be closely related and monoclonal); (ii) if patterns differed by between four and six bands, the strains were scored as being posssibly related but were, nevertheless, classified into distinct genotypes to discriminate them from the closely related strains; and (iii) if patterns differed by seven or more bands, strains were considered to be different. Major genotypes are designated by Arabic numerals. Strains with undistinguishable patterns were classified within the same subtype. Subtypes are designated by Arabic numerals with letter suffixes.
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FIG. 1. Pulsed-field gel electrophoresis of SmaI-digested total DNA from SGAr S. aureus clinical isolates. Lanes A, G, M, and R, NCTC 8325 used as standard; lane B, genotype 17a strain; lane C, genotype 15a strain; lane D, genotype 17c strain; lane E, genotype 16b strain; lane F, genotype 17b strain; lane H, genotype 24h strain (Paris-A, 1997); lane I, genotype 24a strain; lane J, genotype 24a strain (Toulouse, 1998); lane K, genotype 24c strain (Paris-A, 1999); lane L, genotype 30a strain; lane N, genotype 30b strain; lane O, BM3318; lane P, BM3093; lane Q, BM10692.
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PCR. DNA was amplified by PCR by using the Ready-To-Go kit (Amersham) according to the manufacturer's instructions in a Crocodile III apparatus (Appligène, Illkirch, France). The primers used to detect antibiotic resistance genes were those described previously: vatA (8), vatB (4), vgaB (2), and vgbA (7). A DNA fragment from within vgaAv (19) was amplified with primer A (5'-CTCCGTGTTGAAGATGTTTCG-3'; nucleotides [nt] 5881 to 5901; accession no. AF186237) and primer B (5'-GGATTCAAACGCCTCTATAGCC-3'; nt 6339 to 6318; accession no. AF186237). The pIP1680 DNA fragment extending from pAMß1 repE-like gene to vatA was amplified with the primers RepE (5'-ATTGCTGAAGGTACTGAAGG-3'; nt 4343 to 4362; accession no. AF007787) and VatA2 (5'-CAATGACCATGGACCTGATC-3'; nt 269 to 288; accession no. L07778). PCR experiments were carried out at high stringency (initial cycle of 5 min at 95°C and 2 min at 55°C, followed by 35 cycles of 1 min at 72°C, 30 s at 95°C, and 1 min at 55°C, with a final extension step of 5 min at 72°C).
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A total of 46 of the 62 SGAr S. aureus isolates studied were MRSA (74.2%) (Table 1). These MRSA isolates could be divide into gentamicin-sensitive (GENs) and GENr phenotypes (30 and 16 strains, respectively), whereas 9 of the 16 methicillin-susceptible S. aureus (MSSA) isolates were GENs. Eighteen of the MRSA isolates (39.1%) and none of the MSSA isolates were spectinomycin resistant. Pefloxacin-resistant and rifampin-resistant strains were more prevalent among MRSA than among MSSA. Indeed, 40 of the 46 (87%) MRSA isolates were pefloxacin-resistant compared to just 7 of the 16 MSSA isolates (43.8%), and 9 of the MRSA isolates (19.6%) were rifampin resistant compared to one of the MSSA isolates (6.3%).
Of the 62 SGAr strains, 5 had reduced susceptibility to teicoplanin and vancomycin; three of these strains were hetero-VISA, and two were glycopeptide-intermediate S. aureus. These strains were isolated in three different hospitals between 1991 and 2001. All of these strains were MRSA and were either resistant or susceptible to GEN and related aminoglycosides. We also detected six teicoplanin-intermediate strains, four of which were MRSA.
Analysis of the SmaI patterns. As shown in Table 1, the 62 SGAr isolates were distributed into 38 distinct genotypes based on the comparison of SmaI patterns, and each genotype included between 1 and 11 isolates. Although grouped into distinct genotypes, the strains in the following genotypes may have been related because their SmaI patterns differed by six bands or less: genotypes 1 and 2; 16 and 17; 18 and 19; 20 and 21; 22 and 23; 24, 25, and 26; 28 and 29; and 30 and 31. It is noteworthy that major clonal diversity (20 genotypes) was observed among the 30 isolates from one hospital (Paris-A). Some of the isolates belonging to the same genotype were isolated in distinct hospitals located in different cities (12a and 12b, 17a and 17b, 24a to 24h, and 30a and 30b) and/or had different antibiotypes (14a and 14b; 15a to 15c; 24a, 24c, 24g, and 24h; 30a and 30b). Some strains grouped in the same genotype were also disseminated over fairly large time scales (15a in 1991 and 15b in 1999; 30b in 1988 and 30a in 1999).
Distribution of the streptogramin resistance genes tested. In addition to the eight SGAr genes tested, we looked for the presence of vgbA and vgbB, which are frequently localized on SGAr plasmids. We detected vgaAv in 37 of the 62 SGAr strains analyzed (59.7%). These strains were isolated between 1981 and 2001. vgaAv was found alone in 21 strains, in association with vgaB-vatB in 14 strains, in association with vatA-vgbA in 1 strain, and in association with vgaB-vatB and vatA-vgbA in 1 strain. In this latter strain, we confirmed the presence of each of these resistance genes by using PCR to amplify the cellular DNA of a single colony. Of the 25 isolates that did not carry vgaAv, 24 contained vatA-vgbA and 1 contained vgaA alone. Thus, we detected at least one SGAr determinant in each of the 62 SGAr clinical isolates investigated. None of the isolates carried vatC, vatD, vatE, or vgbB.
We measured the sizes of the HindIII fragments that hybridized with the intragenic streptogramin resistance probes. Clinical isolates with the same hybridization pattern did not necessarily belong to the same genotype. In the 21 strains carrying only vgaAv, this gene was carried by HindIII fragments of 0.6 + 1.3 kb (18 isolates), 0.6 + 1.3 + 3 kb (1 isolate), 0.6 + 1.3 + 4.2 + 8 kb (1 isolate), and 0.6 + 5 kb (1 isolate). Two of these profiles were identical to those of S. aureus strains BM3327 (0.6 + 1.3 kb) and BM3252 (0.6 + 1.3 + 3 kb) (19), which carry one and two chromosomal copies of Tn5406, respectively (20). In the 14 strains carrying vgaAv and vatB-vgaB, we found three HindIII patterns with vgaAv: 0.6 + 1.1 kb (10 strains), 0.6 + 1.1 + 1.3 kb (3 strains), and 0.6 + 1.1 + 2.5 (1 strain). Two of these profiles were not distinguishable from those of S. aureus strains BM3318 (0.6 + 1.1 kb) and BM3385 (0.6 + 1.1 + 1.3 kb) (19), which carry either one plasmid copy or one chromosomal copy and one plasmid copy of Tn5406, respectively (20). In each of the 14 strains containing vgaAv-vatB-vgaB, a single HindIII fragment hybridized with both vatB and vgaB. The size of this fragment varied (4.5, 5, 5.5, 7.5, and 9.5 kb). In S. aureus BM3385, in which vatB and vgaB were shown to be cotranscribed (2), the two genes were located on a 7-kb HindIII fragment (results not shown).
In each of the 26 strains containing vatA and vgbA, associated or not with other genes (vgaAv in one isolate and vgaAv-vatB-vgaB in one isolate), vatA and vgbA were found on a single HindIII fragment of 8 or 9.5 kb, whereas in the seven native vgaA-vatA-vgbA plasmids tested previously (3), the cotranscribed genes, vatA-vgbA, were on a 4.8-kb HindIII fragment.
Plasmid content of the SGAr strains carrying vatA-vgbA. Plasmids were extracted from the 26 strains carrying vatA-vgbA and probed with vgbA (pIP1654) and IS257tnp (pIP1644). The extrachromosomal bands (Fig. 2A) that hybridized with both probes had the same apparent sizes and were located just below the chromosomal DNA fragments of the uncleaved total cellular DNA (Fig. 2B). The hybridization patterns with vgbA of these plasmids cleaved by HindIII (results not shown) were identical to those observed with the cellular DNA cleaved by the same enzyme (8 and 9.5 kb). In 5 isolates collected in two hospitals in 1998 and 1999, the cohybridizing band was 8 kb, whereas in 21 isolates collected in seven hospitals between 1988 and 2001 the cohybridizing band was 9.5 kb. The plasmids generating 8-kb HindIII fragments hybridizing with vgbA seem to have emerged later.
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FIG. 2. Agarose gel electrophoresis patterns of plasmid DNA from SGAr S. aureus clinical isolates carrying vatA-vgbA (lanes C to J). (A) Plasmid migration patterns; (B) hybridization patterns with the vgbA probe (pIP1654). Lanes A, the Raoul marker (Appligene) used as a standard; lanes B, total DNA from BM3093; lanes C, plasmid DNA from genotype 22a strain (Paris-A, 1998); lanes D, plasmid DNA from genotype 36a strain; lanes E, plasmid DNA from genotype 8a strain; lanes F, plasmid DNA from genotype 32 strain; lanes G, plasmid DNA from genotype 3 strain; lanes H, plasmid DNA from genotype 19 strain; lanes I, plasmid DNA from genotype 20 strain; lanes J, plasmid DNA from genotype 16a strain.
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All of the staphylococcal isolates tested contained at least one SGAr gene. This finding is consistent with our previous findings concerning another collection of 52 SGAr independent staphylococci belonging to five species (1, 19). Since some of the clinical isolates in both collections carried several SGAr genes, we cannot rule out the possibility that staphylococci contain unknown genes, whereas among E. faecium strains new genes have to be characterized. In the study by Werner et al. (34), 7 of the 148 E. faecium isolates resistant to the mixtures did not contain any of the SGAr genes described to date and in the study by Soltani et al. (29), 8 of the 28 E. faecium mixture-resistant isolates did not contain any of these genes. Despite the multiplicity of unrelated clones detected in the present study, only six distinct SGr patterns were found. This may be due to the dissemination of structurally related plasmids in independent clones, as reported previously (3, 9). The vatA and vgbA combination was not detected in our previous study (1), in which vgaA was always associated with vatA-vgbA. A comparative analysis of seven native vatA-vgbA-vgaA plasmids (15 to 45 kb) revealed the presence of a common 12.1-kb fragment carrying the three streptogramin resistance genes (3). This probably resulted from integration of a pAMß1-like plasmid harboring vatA-vgbA in which the replication gene is inactivated by IS257 insertion and a functional vgaA plasmid. A deletion between IS257 flanking vgaA may have resulted in the formation of vatA-vgbA plasmids (Fig. 2A). The fact that these plasmids have the same size and are found in 42% of the isolates studied here is striking.
Zarrouk et al. (36) reported that the staphylococcal strains resistant to A compounds but susceptible to B compounds remain susceptible to mixtures in vitro and in vivo. According to our previous (19) and present results, this is true when the strains carry vgaAv alone but not when they carry three SGAr genes. Indeed, the 14 SGBs isolates harboring vgaAv alone and originating from two hospitals (Paris-A and Toulouse) had the lincosamide and streptogramin A resistance phenotype. Like BM3385, the two lincosamide and streptogramin A-resistant isolates (genotypes 2 and 14a) (Table 1) that were susceptible to SGB and carried vgaAv, vatB, and vgaB were resistant to the mixtures (Table 1). Four of the seven HindIII hybridization patterns detected with vgaAv were identical to those of previously analyzed S. aureus clinical isolates in which vgaAv was shown to be carried by Tn5406 (19, 20). These results reflect a multiplicity of Tn5406 insertion sites in the collection of isolates tested.
We have found 45 antibiotypes among the SGAr clinical isolates tested. Some of them, such as genotypes 3 and 28 (Table 1), were suceptible to almost all other antibiotics, whereas genotype 15a, 15c, and 35 isolates were multiply resistant to various drugs, including glycopeptides (Table 1). The SmaI pattern of the genotype 15a isolate was identical to that of the major clone with reduced glycopeptide susceptibility found in European cities (17, data not shown). Coresistance to quinupristin-dalfopristin and glycopeptides (33), as in 5 of the 62 clinical isolates tested (8%), is of great concern since it may lead to therapeutic failure.
Since 1975, monoclonal staphylococcal isolates resistant to mixtures of the A and B compounds have occasionally been detected in the same hospitals or in hospitals located in geographically distinct French cities (15). However, in most French hospitals the prevalence of such isolates does not exceed 5% (14). The moderate use of natural mixtures in intensive care units, in which MRSA clinical isolates are easily spread, and the instability of SGAr plasmids, which are frequently lost or rearranged in the absence of selective pressure (1, 3), may explain why the numerous distinct isolates found in French hospitals have not disseminated often. The possible dissemination of such clones with the increased selective pressure of streptogramins after the recent licensing of quinupristin-dalfopristin has to be prevented by improving hygiene and patient isolation measures.
For part of this work, J. Haroche received grants from the Fondation Bayer Santé and from CANAM (Caisse Nationale d'Assurance Maladie et Maternité des Travailleurs Non Salariés des Professions Non Agricoles).
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